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A pattern clustering algorithm is proposed in this paper as a statistical quality control technique for diagnosing the solder paste variability when a huge number of binary inspection outputs are involved. To accommodate this goal, a latent variable model is first introduced and incorporated into classical logistic regression model so that the interdependencies between measured physical characteristics and their relationship to the final solder defects can be explained. This probabilistic model also allows a maximum-likelihood principal component analysis (MLPCA) method to recognize the dimension of systematic causes contributing to solder paste variability. The correlated measurement variables are then projected onto the reduced latent space, followed by an appropriate clustering approach over the inspected solder pastes for variation interpretation and quality diagnosing. An application to a real stencil printing process demonstrates that this method facilitates in identifying the root causes of solder paste defects and thereby improving PCB assembly yield.